Naegi Ex Machina: Danganronpa Another Episode 2
by King Codrian Drasil
Summary: Things are getting back to normal after the events at Jabberwock. But when Makoto Naegi is tasked with battling Monokuma Units, he learns a stunning secret about himself. Post-SDR2. Naegiri. Rated MA for swearing, violence, and possible gore and lemon.
1. Chapter 1

_**Danganronpa: Naegi's Got a Glitch**_

Naegi had no clue as to where he was. All he could see was a thick blackness that was only pierced through by a low fog that reached to his knees. He was genuinely lost, wondering what the hell was happening… in front of him, however, landed some broken cuffs and chains that, for some odd reason, appeared glitched. Before he could ask himself what those chains came from, he looked back up. In front of him was a glitchy door, blood red in appearance. So THAT was where the chains came from… Naegi was visibly afraid at this point, as the door slowly opened. A pair of eyes with red irises pierced through the infinite darkness inside the doorway… a black smoke emerged from the doorframe, and started to envelop the young man…

"Oh my GOOOOOOOOOOOOOOOOOOOOD!" Naegi screamed as he snapped awake in a cold sweat, finding himself in his own bed, in his Future Foundation dorm. He quickly looked around his room, expecting to find someone there. No one appeared to him, however.

"It was just a dream…" he spoke to himself before falling back to sleep, albeit a bit uneasily… The next morning, he awoke once again, this time by his alarm clock. The ahoge stretched and got up from his bed, getting ready for the day. As he brushed his teeth, he could swear that his eyes flashed red for a second, but shrugged it off and continued his routine.

He entered the Foundation's mess hall, where all of the agents went to eat. He went with the simple pancake breakfast, not wanting much after last night's episode. The Division Leader quickly spotted the Executives' Table, where his friends sat, and took his seat.

"Good morning, Naegi-san" Kyouko spoke first, causing Naegi to blush a little. He'd been so used to being referred to by the '-kun' suffix, but since his promotion, Kirigiri had been using '-san' out of subordinate obligation… and he was still getting used to it.

"Naegs, what's up?" Hagakure added, followed by Asahina. "Did you sleep well?"

"I slept fine. Thank you for asking" Naegi responded with a smile… a slightly forced one. There was no way in hell he was telling them what happened last night. Kirigiri threw a suspicious glance at him, but then returned to the conversation. Togami, of course, remained silent. Even if he was made to eat at the same table, he still had a touch of social awkwardness- not in the embarrassing way, but in the fact that he maintained an aloof disposition.

The group ate their breakfast in their usual manner, with light-hearted conversation going on between the four participants. They talked about how the world was starting to look normal again, how businesses and facilities such as supermarkets, schools, and hospitals were springing back up. Naegi felt good knowing that his group's work- and effectively his own as well- was making a difference. However, Nagito Komaeda had come to the table, followed by Hajime Hinata. Naturally, Komaeda was in cuffs and chains- he was insane, both figuratively AND literally. Naegi, without even realizing it, became bitter.

"Sorry, Boss… Trash-kun here wanted to see you, and he wouldn't stop bugging us if we didn't…" Hinata told the other Ahoge.

"Good lord… hello, Komaeda…" Naegi sighed dejectedly, looking at the sociopath.

"Master of Hope, it's good to see you! I'm such a big fan of you!" Komaeda greeted before going into a long ramble about how he tried to model himself after the Ultimate Hope… while things like this were flattering for the most part, when it came from Komaeda- who had intentionally tried to ruin things just for the sake of fueling 'hope'-, he felt insulted. Disgraced, even.

Komaeda had finally reached the end of his ramble, finishing with the statement, "I'm so glad to be a follower of your hope!"

That was it. While he had been able to take Komaeda's rambles before, he just couldn't do it anymore… and as soon as he finished, he said something so uncharacteristic of himself that Kyouko- and even Togami- looked at him in shock…

"… My god, do you EVER FUCKING SHUT UP, YOU TRASH-ASS PIECE OF SHIT?! YOU ARE NOTHING LIKE ME! DON'T EVEN TALK TO ME, YA DAMNED SOCIOPATH!" he bellowed as he slammed his fists against the table, making the plates jump off the table for a second. A few seconds later, he covered his mouth, bewildered at what just came out of it.

"Did… that just come out of MY mouth?!"

"Yes… at a very loud volume, might I add…" Kyouko responded bluntly, a bit worried. "Are you SURE you slept fine, Naegi-san? I-I can… you know… cover for you if you're not feeling well…"

"Sorry… I'm fine… just woke up on the wrong side of the bed, I guess…" Makoto shrugged ashamedly, watching Hinata back away slowly with a visibly scared Komaeda.

 _ **Future Foundation: 11:00 AM**_

Naegi entered the office of Chairwoman Maki Shiranui, ready for what she had to say.

"Come in, Agent Naegi…" she spoke with a professional tone. The young man took his seat in front of her desk, as she shuffled some papers. "You are aware of what occurred in Towa City, right?"

"Yes, Ma'am… I know all too well…" he responded, a bit of venom in his tone in response to those events.

"I know you've been promoted to Division Leader- mainly because of that bet Kirigiri made-, and are thus required to stay at your division… however, I need you to do one last field operation; something I trust you would like to do…" she began, turning her chair to the side and looking at the ceiling. "… I need you to go to Towa City and round up any survivors that are hiding there- your sister and Agent Fukawa included."

Before she could speak any further, Naegi had prepared himself to head out, signaling that he accepted the mission. Without hesitation, she grabbed his shoulder.

"I understand you're gung-ho about this, but even with the Monokuma Units mostly destroyed, we still don't know what could be lurking there… which is why I need you to come with me to the weapons bay..."


	2. Chapter 2

The clouds passed by as Naegi rode a Foundation Chopper to his newest destination: a town in somewhat close proximity to Towa City. This would be good practice for his newest tech, Shiranui told him. He took a look at his right arm, which had a cannon-like arm band that went up almost to his elbow. On his back was a backpack-like device that seemed related to the arm band.

"So, remind me again what this thing is?" Naegi spoke through his scouter-like communicator, a bit confused.

"That, Agent Naegi, is a highly-developed Bullet Converter System, or the Bullet Pack. It uses verbal command to convert energy into tangible ammunition. We've also equipped you with the scouter you're wearing, that allows not only communication with HQ, but also allows you to scan foes for weak points. You can also see things invisible to the naked eye, with the upgrades we have planned soon" Shiranui responded in kind. "You're almost at Ikaku Town. That's where your first mission is."

As they spoke, the chopper landed atop one of the buildings. As Naegi disembarked, he observed his surroundings- ruined, just like he had expected. This place was in definite need of repairs, he could tell that much.

"Alright, your most standard ammo is the Attack Bullet. Since it's a standard program, ammunition for this mode is infinite. We don't want you running out in the heat of battle… to activate the pack, shout 'Attack On'. After that, all you need to do is pull the trigger when need be."

Naegi nodded and complied with her instructions. "Attack On!" he spoke, as the arm cannon began to glow blue along certain areas. A small smile came to his face. He was impressed with what he saw. Afterwards, another voice came through his scouter… a familiar voice.

"Alright, Naegi, you'll need to go down to ground level. Chances are that's where most of the survivors would be."

"Kirigiri! You're there, too?"

"Indeed. Chairwoman Shiranui called me to navigate you through your assignment. There is an access elevator to the right of you. Take it to the first floor."

The brunet young man entered the elevator and rode it down to his first checkpoint... upon reaching it, however, he heard a rustling come from a room adjacent to the lobby he had just entered.

"Naegi, I'm already picking up a bogey to the left of the lobby. Proceed with caution." Kirigiri's voice was stoic as ever, but he still picked up a hint of urgency. Naegi slowly proceeded towards the source of the sound, his cannon ready to fire. Slowly, he opened the door, peering inside before walking in.

"This place gives me the creeps already…" he muttered to himself as he looked around the room. The rustling grew louder as he crept further inwards, until he could make out a faint red glow in the shadows. An eerie silence dragged on and on, as he inched closer towards the shadows…

… Out of nowhere, a black-and-white bear leapt forth, just barely missing Naegi before skidding in front of the door.

"What the hell?! I thought the Monokuma Units were dealt with!" the Ultimate Hope spoke before firing at the monochrome robot, knocking it back a bit. He kept up his fire, continually pelting the bear before it decided to take evasive measures.

"Damn… this thing doesn't wanna quit…" he spoke as he waited for an opening. As he searched, he felt himself getting more and more irate, like something inside him was boiling to insanely high levels… the Monokuma jumped forth at him at full speed, only to receive an Attack Bullet to the face, destroying it in a small explosion.

Naegi sighed, trying to calm himself from the whole ordeal, and scanned around for something to go by. Finding an exit that led into the streets, he quickly bolted for it and ended up in what was once a shopping district. More Monokuma Units were dispersed throughout the area, and not just a few- many of them. The young Hope growled and blasted through the mobs of Monokumas, evading their deadly claws and teeth as he made his way through.

"Wow. Agent Naegi is a surprisingly excellent marksman" Shiranui spoke up.

"Well, Truth Bullets ARE his motif…" Kyouko responded with a faint semblance of a proud smile… and a light purple-ish tint to her cheeks… he couldn't tell through the scouter, sadly… "Anyway, your target destination is in the Bank. It's just a few blocks ahead of your current location."

The young man sped through to the bank, blasting through the Monokumas until they no longer followed or blocked. As he reached the door, a chill ran down his spine… a sense that something horrible was about to happen… it wasn't quite despair, but it was still something dark… he shrugged it off before entering the bank. Unsurprisingly, he was met with more Monokumas, but they seemed… different. They weren't running wild and free like the others… no, they appeared to be more organized. They held several humans as hostages, children included in their sick capture.

"Alright, bears! The bosses want these hostages hauled off to the camps!" a particular Monokuma spoke… this one was somewhat larger than the others in the bank lobby, and he had a red star on the white oval that was his belly. The Monokuma, presumably the leader of the little gang, turned his attention to Naegi… but instead of attacking in a feral manner, he merely welcomed the young man. "Why, hello! You must be Makoto Naegi!"

"And you must be the Monokuma holding people up here… you're about to get demolished, so why not give up now?" Naegi responded, his fists clenched in anger as he approached the bear.

"I wouldn't be so sure of that… I have an important message from the Boss!" With that, the robotic bear pulled up a screen that showed a silhouette against a bright background. One eye was like the Monokuma Red Eye, while the other was hazel… that was all Naegi could make out.

" _Makoto Naegi… it's a pleasure to finally meet the Ultimate Hope! Sadly, I can't be there in person"_ the voice spoke through the projection, its voice a tandem that somehow still had charisma. _"I was waiting for you to come here!"_

"What do you want, you sick bastard?!" Naegi growled, unamused with this new character.

" _Hey, there's no need to be so hostile… I just wanted to provide you with a little challenge. A_ game _, if you will… take a look as I pan the camera to my right…"_

The screen panned to the left, and showed two girls in chains… two familiar girls…

"Komaru! Fukawa!" the young man yelled as his blood boiled even more. "What have you done with them?!"

" _Nothing yet… but here's where my game comes in. All throughout the globe, I have my five High Guards stationed, positioned to wreak despair. Your job is to stop them. If you can do that much, I'll let you know where MY lair is, and you can have a chance to save your precious sister and friend. But here's the twist… you have three months to do so. If you can't do it in time, well… try to adjust to not having a family if you manage to survive…"_

That was it. That pushed him past his breaking point… whoever this fucker was, he was gonna get it.

"You bastard… you DAMN bastard…"

" _You're too kind… Monokumas, mob him."_ The projection stopped, and the Monokumas started to surround the Hope Agent… until they dogpiled atop him in a manner similar to a bee swarm.

"NAEGI!" both Shiranui and Kirigiri bellowed in fear, watching him get mobbed… until a low chuckle came from their speakers.

" **Heheheh… now you've done it, Mr. Shadow Fuck…"** the voice spoke sinisterly. The pile of Monokumas started to wiggle a bit… then the wiggling became a rumble as it slowly rose up. Without even the slightest warning afterwards, the robotic bears were launched in all directions. Standing where Naegi was… no one could have seen coming…

There stood Naegi, hunched over as if he were a zombie… his chocolate-brown hair had turned a pitch black, as had his suit. The tie was now red, and an eerie glow came from him. One Monokuma rushed towards him, its claws bared… and was met with a black, spiked Attack Bullet to the chest. It didn't explode, leaving the black-and-white bear to scream in agony as its circuits were slowly corroded.

Naegi, now standing upright, lifted his head and opened his eyes… they had turned red, with something akin to Enoshima's Insignia lightly encircling his pupils.

" **You know, this story was already rated M, but with you guys being robots, I can be as hardcore as I want!"** this new entity spoke in a sadistic voice, as he gestured for the other Monokumas to come at him- his mouth never changed from the scowl he had. Like the other Monokumas outside, he attacked quickly… only this time, he was considerably more brutal. Arms were torn from the bears' bodies, gears and circuits spilled out of the wounds… the dark Naegi had gotten one of his spiked Bullets and started clubbing the bears with it until their heads were severely dented. The robot bodies piled up as the carnage continued… until only the Red Star Monokuma was left.

Red Star backed away as the now-malevolent young man wandered in its direction. For the first time, his mouth switched from the scowl it once was… to a sadistic grin akin to a serial killer. This wasn't Naegi… he was much more predatory. He quickly grabbed the Red Star Monokuma by what constituted as its throat, and leaned in.

" **Listen here, you furry FUCK! I would kill you, but I need you to deliver a message… tell the guy you work for… I was gonna try and simply capture him, and send him to a correctional facility… I was gonna offer him hope, but he just fucked that chance up. He isn't deserving of the hope I provide. Tell him I'll take him up on his little game. And WHEN I win, I'll hunt him down… and when I'm done with him, he'll BEG for death… tell him Makoto Naegi said that…"** the darkened agent growled as he released the bear, who then proceeded to run away in fear.

Just as it did, though, the young man fell unconscious and collapsed on the floor. His hair returned to its chocolate brown, and his suit and tie turned back to normal as well.

In the Navigation Room that Shiranui was situated in, the Future Foundation Leader looked at Kirigiri in horror… a look that was reciprocated by the latter. Shiranui grabbed the intercom and spoke.

"Transport Team, I need you to get Agent Naegi back here. NOW!"


	3. Chapter 3

The young brunet awoke in an infirmary room, and by the looks of it, he was back at the Future Foundation. But why? He was sent to rescue survivors, so why would they bring him back? And what happened after he was mobbed by the Monokumas? Did he get critically injured? Were the hostages okay? He had to know, so he slowly arose from his bed.

"Have a seat, Agent Naegi…" a voice spoke behind him. He turned his head to see Shiranui sitting on the other side of the bed. A look of concern was spread on her face… he could also make out fear for some reason. He sat back on the bed and faced the woman, wanting to know what just happened.

"First off, are the survivors alright?" he asked.

"They are fine… I had the rescue teams cart them off while the retrieval team got you."

"Okay…"

"What I want to ask you is very simple… what… the fuck… was that stunt you pulled back there?!" she demanded. This wasn't so much a stern order, but rather a show that something happened while he was out… something that was so horrible, it shook her to the core.

"What stunt? I fell unconscious when the Monokumas mobbed me!"

A silence filled the room… it got so quiet, that the two could actually hear their own breathing. Naegi noticed that his boss's breathing was much heavier than his own. Did something happen that scared her THAT much? And did he have something to do with it?

"You mean to tell me… that you don't remember? You don't remember brutally dismembering the Monokuma Units? You don't remember clubbing them to death with hacked Attack Bullets? You don't remember threatening the Red Star Monokuma? You remember none of it?"

Naegi shook his head as he looked her in the eye. It was then that he remembered the proposition that the silhouette made.

"But we don't have time for this… that silhouette that Red Star was working for said I only have three months to travel the world and defeat his five Admins, or else Komaru and Fukawa bite the dust… that's pretty much the last thing I remember…"

Shiranui merely looked at him with a correcting glare. "I understand your predicament, but from the sounds of it, this 'Brutal' you acts completely independent of you, aside from needing your body. If we don't get this resolved, you could become involved in a threat!"

"Chairwoman Shiranui, with all due respect-"

"THE GAME CAN WAIT! YOU NEED ATTENTION!" she barked back, showing more authority this time. This later proved to be a bad move, as when she looked at him again, his hair and suit were black once more, and his eyes were red again.

" **You'd best watch your tongue, Maki. You might just lose it…"** the dark Naegi spoke, before quickly reverting back to normal. The Chairwoman had just gotten enough confirmation to prove her point.

"Shit! I'm sorry, Chairwoman! Did I do something wrong?"

"… This won't take very long. Just… please go to Psycho Analysis… I promise that I'll help you get your sister and friend back, but you need to let me help you…"

The young man complied and arose from the bed, following his boss to Psycho Analysis.

* * *

 _Future Foundation Psycho Analysis_

* * *

"Hmm… yes, I think I understand now. What Naegi is suffering from is a case of Dissociative Identity Disorder…" a man in a lab coat spoke as Naegi got up from the MRI. Inside were Shiranui and Kirigiri, but the others had decided to come and see what the fuss was about. Word had gotten out of the brutality at Ikaku Town, and the group- save for Byakuya- became worried.

"So, he's basically Genocide Jill?!" Hagakure questioned in disbelief.

"If that's the case, then why is his hair black and his eyes red? I heard he underwent physical change" Asahina added.

"The same unexplained reason Fukawa's eyes turn red when she becomes Genocide Jill, I would imagine" Togami was the last to speak.

The quiet started to settle in, with nothing but the beeping of machinery making any noise. This was difficult for Naegi to process, to say the least. He'd just been told that a killer lived inside of him, after all. Sure, it'd only killed robots so far, but how far would it go? It wouldn't surprise him if IT turned towards despair…

"I don't think it's QUITE the same as Genocide Jill…" Kirigiri spoke up, earning the attention of the others. "It seems that this dark persona… this 'Glitch' if you will… it's tethered to Naegi's main personality. Why do you think the Glitch passed out after the Red Star Monokuma ran away?"

"I don't follow, Kirigiri…" Naegi spoke.

"Something is tethering you to this dark personality, and whatever it is, it's causing your main personality to keep the glitch in check" Kirigiri flipped her hair a little as she viewed the video file from the fight. It showed the dark Naegi's speech to Red Star, and then him passing out. She replayed the speech to gain a better understanding of the dark persona's mannerisms and mentality.

"This thing still abides to Naegi's hopeful personality, but infuses it with a Holier than Thou complex. It's like he believes that he's a judge, and that people who cross him are criminals damned to Hell… maybe this can work to our advantage."

The entire room looked at her with bewildered expressions. A couple of people thought she had gone crazy, and started to back away for their own safety.

"What are you on about, Kirigiri?" Togami demanded, baffled by the words that came out of her mouth.

"Think of it like this… Naegi, I know you tend to fall unconscious when this personality- which we shall codename 'Glitch Naegi'- comes into play, so you can't necessarily control it… but perhaps when you feel it starting to surface, you can aim it… but only if you're backed into a corner."

As much as it pained him to think about it, Kirigiri was right. It hadn't harmed any innocent people yet, so it was still too early to discern whether or not this thing was a threat. He mulled it over for a moment, then looked at the lilac-haired girl with an affirmative nod.

"Alright… if it can help get Komaru and Fukawa back, then I guess it's worth a try…"

* * *

The next morning, Naegi prepared himself for a mission, and headed for the Navigation Room. Upon entering, he encountered his friends, who had positioned themselves at certain devices.

"What's going on?" Naegi questioned. Kirigiri came in and sat at her own navigation computer, swiveling the chair towards him.

"They insisted on helping, so Chairwoman Shiranui and I are having them aid in navigation."

The young brunet smiled as the group greeted him, but paused when Shiranui came into the room. Without a single word, she inserted a chip into his Bullet Pack, earning his confusion. The woman sat in her Command Chair and turned to face him.

"I've upgraded your Bullet Pack. This newest update will release waves that will agitate you into becoming Glitch Naegi for a short period of time… however, after a set time limit is reached, the Bullet Pack will release calming waves and revert you to normal. This is still untested, so try not to abuse it… we don't know what overuse will do."

Naegi still felt a little uneasy about this, but nodded affirmative. Shiranui then turned to the Command Screen and searched for the first of the silhouette's Admins. After a few minutes of scanning, the computer pulled up one result. The screen quickly zoomed in on the Western Hemisphere- in particular, North America. High levels of despair were detected in the area.

"I'll try to zero in on the exact location, but your first stop appears to be America. It appears to be more specifically in the Northern region."

Ready for his new mission, Naegi headed for the chopper.

"Just wait, you two… I'll get you out of there…" he spoke to himself.

* * *

 _In an unknown location…_

* * *

The figure from the video stood in the Manhattan Area, perched atop the Statue of Liberty. A sinister grin crept up on his face as another figure, appearing female, approached behind him.

"Shall I go now, Mastermind?" she spoke with a cheeky yet cunning voice.

"Yes, Dark Roulette… our guest should be on his way VERY soon…"


End file.
